Variant report

Variant	rs1970
Chromosome Location	chr6:30125543-30125544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30120236..30122567-chr6:30123683..30125574,2	MCF-7	breast:
2	chr6:30083851..30086480-chr6:30123012..30125789,2	MCF-7	breast:
3	chr6:30034609..30036476-chr6:30124190..30127088,3	K562	blood:

Variant related genes	Relation type
ENSG00000204619	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11158	0.98[EUR][1000 genomes]
rs1264705	0.83[EUR][1000 genomes]
rs1264706	0.83[EUR][1000 genomes]
rs1573296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2023473	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2106072	0.98[EUR][1000 genomes]
rs2157678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2517601	0.84[EUR][1000 genomes]
rs2517609	0.91[EUR][1000 genomes]
rs2517617	0.91[EUR][1000 genomes]
rs2517622	0.98[EUR][1000 genomes]
rs2523712	0.91[EUR][1000 genomes]
rs2523729	0.98[EUR][1000 genomes]
rs2523735	0.81[EUR][1000 genomes]
rs2523978	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2844777	0.88[EUR][1000 genomes]
rs2844789	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094064	0.81[EUR][1000 genomes]
rs3094066	0.85[EUR][1000 genomes]
rs3094067	0.81[EUR][1000 genomes]
rs3094069	0.85[EUR][1000 genomes]
rs3094078	0.85[EUR][1000 genomes]
rs3094628	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3129830	0.85[EUR][1000 genomes]
rs3130355	0.81[EUR][1000 genomes]
rs3130364	0.80[EUR][1000 genomes]
rs3130377	0.80[EUR][1000 genomes]
rs3130380	0.85[EUR][1000 genomes]
rs3130399	0.85[EUR][1000 genomes]
rs8321	0.81[EUR][1000 genomes]
rs9261290	0.80[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1970	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs1970	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30121000-30128200	Weak transcription	Lung	lung
2	chr6:30121600-30125600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:30122200-30128200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:30122400-30125800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:30123000-30126200	Enhancers	NHDF-Ad	bronchial
6	chr6:30123200-30126200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:30124400-30125600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:30124400-30125600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr6:30124400-30125600	Weak transcription	Osteobl	bone
10	chr6:30124400-30130800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:30124800-30127000	Enhancers	GM12878-XiMat	blood
12	chr6:30124800-30127800	Weak transcription	HepG2	liver
13	chr6:30124800-30130200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:30124800-30130200	Weak transcription	Stomach Mucosa	stomach
15	chr6:30124800-30130400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:30124800-30130800	Weak transcription	A549	lung
17	chr6:30124800-30132600	Weak transcription	Right Atrium	heart
18	chr6:30125000-30126600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:30125000-30128200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:30125000-30130200	Weak transcription	Fetal Intestine Large	intestine
21	chr6:30125000-30130200	Weak transcription	Fetal Intestine Small	intestine
22	chr6:30125200-30128400	Weak transcription	Rectal Mucosa Donor 31	rectum

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